Merge branch 'dev' into 'master'

Dev

See merge request xpub/xpub-epmc!172

app/components/activity/ManualCitation.jsx

+import moment from 'moment'
 import { omit } from 'lodash'
 import { compose } from 'recompose'
 import { withFormik } from 'formik'
@@ -36,9 +37,14 @@ const handleSubmit = async (
     }
     if (values.printseason) {
       ppub.jatsDate.season = values.printseason
+      ppub.date = moment.utc(values.printyear, 'YYYY')
     } else {
       ppub.jatsDate.month = values.printmonth
       ppub.jatsDate.day = values.printday
+      ppub.date = moment.utc(
+        `${values.printyear} ${values.printmonth} ${values.printday}`,
+        'YYYY MMM DD',
+      )
     }
     meta.publicationDates.push(ppub)
   }
@@ -51,9 +57,16 @@ const handleSubmit = async (
     }
     if (values.electronicseason) {
       epub.jatsDate.season = values.electronicseason
+      epub.date = moment.utc(values.electronicyear, 'YYYY')
     } else {
       epub.jatsDate.month = values.electronicmonth
       epub.jatsDate.day = values.electronicday
+      epub.date = moment.utc(
+        `${values.electronicyear} ${values.electronicmonth} ${
+          values.electronicday
+        }`,
+        'YYYY MMM DD',
+      )
     }
     meta.publicationDates.push(epub)
   }

app/components/citation-search/PubMedSearch.jsx

@@ -110,6 +110,7 @@ class PubMedSearch extends React.Component {
       if (isDate(result.pubdate)) {
         ppub.date = isDate(result.pubdate)
       } else {
+        ppub.date = moment.utc(result.pubdate.substring(0, 4), 'YYYY')
         ppub.jatsDate = {
           year: result.pubdate.substring(0, 4),
           season: result.pubdate.substring(5),
@@ -122,6 +123,7 @@ class PubMedSearch extends React.Component {
       if (isDate(result.epubdate)) {
         epub.date = isDate(result.epubdate)
       } else {
+        epub.date = moment.utc(result.pubdate.substring(0, 4), 'YYYY')
         epub.jatsDate = {
           year: result.pubdate.substring(0, 4),
           season: result.epubdate.substring(5),

app/components/dashboard/operations.js

@@ -96,10 +96,6 @@ const DashboardFragment = gql`
         type
         date
       }
-      notes {
-        notesType
-        content
-      }
       fundingGroup {
         fundingSource
         awardId

app/components/submission-wizard/CreatePage.jsx

@@ -73,19 +73,6 @@ class Created extends React.Component {
       newReviewer: null,
     }
   }
-  componentDidUpdate(prevProps, prevState) {
-    const { newReviewer } = prevState
-    const { notes } = prevProps.manuscript.meta
-    const reviewerNote = notes
-      ? notes.find(n => n.notesType === 'selectedReviewer')
-      : null
-    if (reviewerNote && reviewerNote.content === JSON.stringify(newReviewer)) {
-      const { id } = this.props.manuscript
-      this.props.setStatus('READY', () => {
-        this.props.history.push(`/submission/${id}/submit`)
-      })
-    }
-  }
   static contextType = UserContext
   getCurrentStep = () => {
     const { meta, files } = this.props.manuscript
@@ -186,6 +173,11 @@ class Created extends React.Component {
       newState.showSearch = false
     } else if (this.state.currentStep < 3) {
       newState.currentStep = this.state.currentStep + 1
+    } else {
+      const { id } = this.props.manuscript
+      this.props.setStatus('READY', () => {
+        this.props.history.push(`/submission/${id}/submit`)
+      })
     }
     this.setState(newState)
     window.scrollY = 0
@@ -310,9 +302,8 @@ class Created extends React.Component {
                             content: JSON.stringify(newReviewer),
                           })
                         }
-                      } else {
-                        this.goNext()
                       }
+                      this.goNext()
                     }}
                     primary={!this.state.showSearch}
                     title={
@@ -359,10 +350,9 @@ class Created extends React.Component {
           </InfoPanel>
           {cancel && (
             <SubmissionCancel
-              cancel={() =>
-                this.props.deleteMan(() => this.props.history.push('/'))
-              }
+              callback={() => this.props.history.push('/')}
               close={() => this.setState({ cancel: false })}
+              manuscriptId={manuscript.id}
             />
           )}
         </SplitPage>

app/components/submission-wizard/Submit.jsx

@@ -170,12 +170,13 @@ class Submit extends React.Component {
         <React.Fragment>
           {(() => {
             if (
-              (reviewer &&
+              !currentUser.admin &&
+              ((reviewer &&
                 reviewer.id === currentUser.id &&
                 !['in-review', 'submission-error'].includes(status)) ||
-              (submitter &&
-                submitter.user.id === currentUser.id &&
-                !['INITIAL', 'READY', 'submission-error'].includes(status))
+                (submitter &&
+                  submitter.user.id === currentUser.id &&
+                  !['INITIAL', 'READY', 'submission-error'].includes(status)))
             ) {
               window.scrollY = 0
               window.pageYOffset = 0

scripts/shared-data-model.sql

@@ -93,7 +93,7 @@ CREATE TABLE manuscript (
 );
 
 -- ALTER SEQUENCE manuscript_id_seq RESTART WITH 80000;
-CREATE SEQUENCE manuscript_emsid_seq START 90000;
+CREATE SEQUENCE manuscript_emsid_seq START 82777;
 
 CREATE INDEX pdfState_idx ON manuscript (pdf_deposit_state);
 

server/ncbi-integration/toNcbi.js

+const moment = require('moment')
 const logger = require('@pubsweet/logger')
 const path = require('path')
 const { exec } = require('child_process')
@@ -164,12 +165,19 @@ function createManifest(tmpPath, manuscript, funders) {
   const pmId = manuscript['meta,articleIds'].find(id => id.pubIdType === 'pmid')
     ? manuscript['meta,articleIds'].find(id => id.pubIdType === 'pmid').id
     : 0
-  const createdDate = new Date(manuscript.created).toISOString().split('T')[0]
-  const publishDate = new Date(
-    manuscript['meta,publicationDates'].find(date => date.type === 'ppub').date,
-  )
-    .toISOString()
-    .split('T')[0]
+  const createdDate = moment(manuscript.created).format('YYYY-MM-DD')
+  const pubDates = manuscript['meta,publicationDates']
+  const releaseDelay = manuscript['meta,releaseDelay']
+    ? parseInt(manuscript['meta,releaseDelay'], 10)
+    : 0
+  const startDate =
+    (pubDates.find(date => date.type === 'ppub') &&
+      pubDates.find(date => date.type === 'ppub').date) ||
+    (pubDates.find(date => date.type === 'epub') &&
+      pubDates.find(date => date.type === 'epub').date)
+  const publishDate = moment(startDate)
+    .add(releaseDelay, 'M')
+    .format('YYYY-MM-DD')
   const hasPubPdf = manuscript.files.find(file => file.type === 'pdf4load')
     ? '1'
     : '0'
@@ -280,8 +288,9 @@ function getFilesPrefix(manuscript) {
 }
 
 function getNcbiFiles(manuscript) {
-  return manuscript.files.filter(file =>
-    ncbiFileTypes.find(type => type.value === file.type),
+  return manuscript.files.filter(
+    file =>
+      !file.deleted && ncbiFileTypes.some(type => type.value === file.type),
   )
 }
 

server/xpub-model/entities/note/data-access.js

 const { Model } = require('objection')
+const logger = require('@pubsweet/logger')
 const uuid = require('uuid')
 const EpmcBaseModel = require('../epmc-base-model')
 const { rowToEntity, entityToRow, buildQuery, runQuery } = require('../util')
@@ -114,11 +115,18 @@ class Note extends EpmcBaseModel {
     return manuscript
   }
 
-  static delete(id, userId) {
-    return Note.query().updateAndFetchById(id, {
-      deleted: new Date().toISOString(),
-      updatedBy: userId,
-    })
+  static async delete(id, userId) {
+    try {
+      await Note.query().updateAndFetchById(id, {
+        deleted: new Date().toISOString(),
+        updatedBy: userId,
+      })
+      logger.info('Note deleted')
+      return true
+    } catch (err) {
+      logger.error('Note delete error: ', err)
+      return false
+    }
   }
 
   static async deleteByManuscriptId(id, userId, trx) {